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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgctggagatcttcgtttgtcttgacaatcctttctcgtgatttgagctaatgtgtgcatgtttaccggtccaatctttttacgaaagaacacttggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAATTCGATGTCAACCAGGTTGAGTTGTGTATGGTCAATTGGCTCCCAGGATC

Basic information

species Physcomitrella patens
transcript PP1S41_235V6.1
intron # 19
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37832974|gb|BJ590986.1|BJ590986
EST:     GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACG                         GCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
genomic: GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACGgtgagctgct ... ggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
EST: gi|37829873|gb|BJ587885.1|BJ587885
EST:     GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACG                         GCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
genomic: GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACGgtgagctgct ... ggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
EST: gi|37830724|gb|BJ588736.1|BJ588736
EST:     GTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAANCG                         GCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
genomic: GTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACGgtgagctgct ... ggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
EST: gi|18336891|gb|BJ168914.1|BJ168914
EST:     GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACG                         GCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
genomic: GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACGgtgagctgct ... ggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
EST: gi|18339547|gb|BJ171574.1|BJ171574
EST:     GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACG                         GCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT
genomic: GACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACGgtgagctgct ... ggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 23 (downstream exon)
Score: 2

TCCATGGTGGAGTACACTGCCATTGATGGTACTGAGCATATACTTCGAGCGACCACGGGAGTTGCAGAAATGGTGTTCACCGGTGACAGCAGACCAAACGgtgagctgct ... ggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAATTCGATGTCAACCAGGTTGAGTTGTGTATGGTCAATTGGCTCCCAGGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtgcatgtttaccggtccaatctttttacgaaagaacacttggatgtgcagGCGAATGGATGCTTGTGGATAATCAAACTGGTCTGGCGGTGGTGAACAAATTCGATGTCAACCAGGTTGAGTTGTGTATGGTCAATTGGCTCCCAGGATC
 agctaat  putative branch site (score: 2)
                      aatcttttta  TA-rich tract